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The Mozilla Toolkit is a set of APIs, built on top of Gecko, which provide advanced services to XUL applications. These services include Profile Management, Chrome Registration, Browsing History, Extension and Theme Management, Application Update Service, and Safe Mode. (More info)

I think simply overriding is always a bad idea, even if there is a permission. Firefox should finally get a proper UI for configuring keyboard shortcuts where conflicts are visible and resolvable in a clever way.

Bug 1303384 is about providing a UI for re-assigning command shortcuts. Probably the only thing this adds to that bug is showing the built in commands so you can see when a shortcut is overriding a build in shortcut.